The present review is focused on the current role of neoplastic stem and progenitor-like cells as primary targets in the pharmacotherapy of cancer as well as in the development of new anticancer drugs. We begin by summarizing the main characteristics of these tumor-initiating cells and key concepts that support their participation in therapeutic failure. In particular, we discuss the differences between the major carcinogenesis models (ie, clonal evolution vs cancer stem cell (CSC) model) with emphasis on breast cancer (given its importance to the study of CSCs) and their implications for the development of new treatment strategies. In addition, we describe the main ways to target these cells, including the main signaling pathways that are more activated or altered in CSCs. Finally, we provide a comprehensive compilation of the most recently tested drugs.